Center for Applied Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Appl Environ Microbiol. 2019 Mar 6;85(6). doi: 10.1128/AEM.02768-18. Print 2019 Mar 15.
Dichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader " Dichloromethanomonas elyunquensis" strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/cofactor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM's genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase of strain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase of sp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway. Naturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader " Dichloromethanomonas elyunquensis" strain RM, suggesting that reductive dechlorination and methyl group transfer play roles in anaerobic DCM degradation. These findings suggest that the characterized DCM-degrading bacterium and " Dichloromethanomonas elyunquensis" strain RM utilize distinct strategies for carbon-chlorine bond cleavage, indicating that multiple pathways evolved for anaerobic DCM metabolism. The specific proteins (e.g., RDases and methyltransferases) identified in strain RM may have value as biomarkers for monitoring anaerobic DCM degradation in natural and contaminated environments.
二氯甲烷（DCM）在缺氧条件下易被微生物降解，并通过 Wood-Ljungdahl 途径代谢；然而，碳-氯键断裂的机制理解仍有所欠缺。微生物联合体 RM 中含有 DCM 降解菌“Dichloromethanomonas elyunquensis”菌株 RM，该菌严格以 DCM 作为生长基质。应用于 DCM 培养的联合体 RM 生物量的蛋白质组学工作流程共揭示了 1705 种非冗余蛋白，其中 521 种可分配给菌株 RM。在 DCM 存在的情况下，菌株 RM 表达了完整的 Wood-Ljungdahl 途径酶，以及与趋化性、运动性、孢子形成和维生素/辅酶合成相关的蛋白质。四种钴胺素依赖性甲基转移酶是最丰富的蛋白质之一。值得注意的是，菌株 RM 基因组中编码的三种假定还原脱卤酶（RDases）中有两种也被检测到高丰度表达。表达的 RDase1 和 RDase2 具有 30%的氨基酸同一性，RDase1 与菌株 WBC-2 的 RDase 最为相似（AOV99960，52%的氨基酸同一性），而 RDase2 与 sp. 菌株 UNSWDHB 的 RDase 最为相似（EQB22800，72%的氨基酸同一性）。虽然 RDases 参与厌氧 DCM 代谢尚未通过实验验证，但蛋白质组学特征表明可能涉及一个或多个还原脱氯步骤和甲基转移反应，从而对厌氧 DCM 降解途径提出了修订建议。自然产生和人为释放的 DCM 可以存在于缺氧环境中，但在没有氧气的情况下，关于参与碳-氯键断裂的生物体、酶和机制的多样性知之甚少。通过蛋白质基因组学方法鉴定出由 DCM 降解菌“Dichloromethanomonas elyunquensis”菌株 RM 表达的两种 RDases 和四种钴胺素依赖性甲基转移酶，表明还原脱氯和甲基转移在厌氧 DCM 降解中发挥作用。这些发现表明，所研究的 DCM 降解菌和“Dichloromethanomonas elyunquensis”菌株 RM 利用不同的策略进行碳-氯键断裂，表明为厌氧 DCM 代谢进化了多种途径。在菌株 RM 中鉴定出的特定蛋白质（例如 RDases 和甲基转移酶）可能作为监测自然和污染环境中厌氧 DCM 降解的生物标志物具有价值。
